NgsCcts

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== Microbiome ==  
 
== Microbiome ==  
 
* [[QIIME 1.5]]
 
* [[QIIME 1.5]]
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== R-packages ==
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* [[R-packages]]
  
 
== Alignment Visualization ==
 
== Alignment Visualization ==
* [http://www.broadinstitute.org/software/igv/download IGV] [http://www.broadinstitute.org/igv/projects/downloads/igvtools_2.1.7.zip 2.1.23]
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* [http://www.broadinstitute.org/software/igv/download IGV]
* [http://www.broadinstitute.org/software/igv/download igvtools] [http://www.broadinstitute.org/igv/projects/downloads/igvtools_2.1.7.zip 2.1.7]
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** [http://www.broadinstitute.org/igv/projects/downloads/igvtools_2.1.7.zip IGV 2.1.23]
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* [http://www.broadinstitute.org/software/igv/download igvtools]  
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** [http://www.broadinstitute.org/igv/projects/downloads/igvtools_2.1.7.zip IGVtools 2.1.7]
  
 
== Short Read Aligners ==
 
== Short Read Aligners ==
 
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* [ tophat]
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** tophat-2.0.6 [http://tophat.cbcb.umd.edu/downloads/tophat-2.0.6.Linux_x86_64.tar.gz (binary)]
 
* [http://bowtie-bio.sourceforge.net bowtie]
 
* [http://bowtie-bio.sourceforge.net bowtie]
 
** bowtie-0.12.7 (linked from Galaxy)
 
** bowtie-0.12.7 (linked from Galaxy)
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** bowtie-0.12.8 [http://downloads.sourceforge.net/project/bowtie-bio/bowtie/0.12.8/bowtie-0.12.8-linux-x86_64.zip?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fbowtie-bio%2Ffiles%2Fbowtie%2F0.12.8%2F (binary)]
 
* [http://bowtie-bio.sourceforge.net/bowtie2 bowtie2]
 
* [http://bowtie-bio.sourceforge.net/bowtie2 bowtie2]
** bowtie2-2.0.0-beta7 [http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.0.0-beta7/bowtie2-2.0.0-beta7-linux-x86_64.zip?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fbowtie-bio%2Ffiles%2Fbowtie2%2F2.0.0-beta7%2F&ts=1349813862&use_mirror=superb-dca3 bin download]
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** bowtie2-2.0.0-beta7 [http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.0.0-beta7/bowtie2-2.0.0-beta7-linux-x86_64.zip?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fbowtie-bio%2Ffiles%2Fbowtie2%2F2.0.0-beta7%2F&ts=1349813862&use_mirror=superb-dca3 (download binary)]
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* bwa
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** bwa-0.6.2 [http://downloads.sourceforge.net/project/bio-bwa/bwa-0.6.2.tar.bz2?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fbio-bwa%2Ffiles%2F&ts=1349814953&use_mirror=iweb (download src)] [[NgsCctsBuildBwa]]
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* MOSAIK
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** mosaik-1.1.0021 - installed in galaxy
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** mosaik-2.1 exe_dist too old, must build from source [https://mosaik-aligner.googlecode.com/files/MOSAIK-2.1.73-source.tar (download src)] [[NgsCctsBuildMosaik]]
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== Short Read (denovo) Assemblers ==
 
== Short Read (denovo) Assemblers ==
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* [http://www.ebi.ac.uk/~zerbino/velvet velvet ]
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** velvet_1.2.08 ([http://www.ebi.ac.uk/~zerbino/velvet/velvet_1.2.08.tgz download src])([[NgsCctsBuildVelvet]])
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*** MAXKMERLENGTH = 57
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*** LONGSEQUENCES
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== SNP analysis ==
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* [http://snpeff.sourceforge.net/index.html SnpEff]
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** snpeff_3_1 ([http://sourceforge.net/projects/snpeff/files/snpEff_v3_1_core.zip/download zip])
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*** scripted install of galaxy wrappers [https://projects.uabgrid.uab.edu/galaxy/browser/tools/snpEff/_install_from.sh galaxy/tools/snpEff/_install_from.sh]
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*** gene indexes for all available genomes downloaded and install
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**** 1112 genomes, 4.8G
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**** data in /scratch/share/public_datasets/ngs/databases/snpEff/3_1/data
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**** parallel download script /scratch/share/public_datasets/ngs/scripts/databases/snpEff/qsub_download_snpEff_genome
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== Pairwise Sequence Alignment ==
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* '''GeneWise''' (compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors)
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** wise2.2.0 [ftp://ftp.ebi.ac.uk/pub/software/unix/wise2/wise2.2.0.tar.gz (donload binary)] [[NgsCctsGeneWise]]
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== Variant Handling ==
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* vcflib https://github.com/ekg/vcflib  [[NgsCctsVcflib]]
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* vcftools
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== in process ==
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* [http://www.bcgsc.ca/platform/bioinfo/software/abyss ABySS] '''NOT DONE'''
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** abyss_1.3.4 ([http://www.bcgsc.ca/downloads/abyss/abyss-1.3.4.tar.gz download src])([[NgsCctsBuildAbyss]])
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*** maxk=100
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* [http://www.broadinstitute.org/scientific-community/science/projects/viral-genomics/viral-genomics-analysis-software?package=VICUNA VICUNA] from Broad Institute ([[NgsCctsBuildVicuna]]) - Viral genome denovo assembler '''NOT DONE'''
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** VICUNA_v1.2 [http://www.broadinstitute.org/software/viral/vicuna/vicuna.zip]
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** V-FAT [http://www.broadinstitute.org/software/viral/vfat/vfat.zip]
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** V-Phaser & V-Profiler [http://www.broadinstitute.org/software/viral/v_phaser/v_phaser.zip]

Latest revision as of 13:19, 24 February 2014

Contents

[edit] Shared CCTS NGS apps

This page documents apps installed by the CCTS BMI group in cheaha:/share/apps/ngs-ccts

Links to latest versions of each package are in /share/apps/ngs-ccts/latest.

See also PublicDatasetsNgs for genomes, indices and databases

[edit] Microbiome

[edit] R-packages

[edit] Alignment Visualization

[edit] Short Read Aligners

[edit] Short Read (denovo) Assemblers

[edit] SNP analysis

  • SnpEff
    • snpeff_3_1 (zip)
      • scripted install of galaxy wrappers galaxy/tools/snpEff/_install_from.sh
      • gene indexes for all available genomes downloaded and install
        • 1112 genomes, 4.8G
        • data in /scratch/share/public_datasets/ngs/databases/snpEff/3_1/data
        • parallel download script /scratch/share/public_datasets/ngs/scripts/databases/snpEff/qsub_download_snpEff_genome

[edit] Pairwise Sequence Alignment

  • GeneWise (compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors)

[edit] Variant Handling

[edit] in process

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